BN1836 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 3.9681e-06 1.7344e-02
Layer 4 1.0907e-05 6.9411e-04
Layer 5 4.4167e-04 2.0506e-03
Layer 2 1.1553e-03 8.9692e-02
Layer 6 1.5898e-03 7.3043e-03
Layer 1 1.8331e-01 3.5334e-01
WM 9.9755e-01 8.8163e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SYT1 Expression Distribution
Gene Specificity Score (GSS)
SYT1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SYT1 Layer 4 2.2578 0.6035
CPLX1 Layer 5 2.2832 0.6016
CALM3 Layer 4 2.1973 0.5955
NEFL Layer 5 2.3398 0.5936
STXBP1 Layer 4 2.4121 0.5877
DNM1 Layer 5 2.1973 0.5844
STMN2 Layer 4 2.6074 0.5841
MORF4L1 Layer 5 2.1973 0.5777
CHGA Layer 4 2.5723 0.5774
UCHL1 Layer 6 2.1289 0.5722
NDRG4 Layer 5 2.4609 0.5715
RTN1 Layer 6 2.3496 0.5709
GHITM Layer 5 2.1055 0.5707
STMN1 Layer 5 2.3555 0.5706
TUBB Layer 5 2.4844 0.5692
FKBP8 Layer 4 2.3652 0.5682
GDI1 Layer 4 2.1582 0.5680
PPIA Layer 6 2.1582 0.5679
ARL6IP1 Layer 5 2.2324 0.5676
SERPINI1 Layer 4 2.5957 0.5668
ATP1B1 Layer 5 2.1348 0.5642
TMSB10 Layer 6 2.0586 0.5633
USP11 Layer 4 2.3809 0.5593
SEPTIN7 Layer 4 2.2832 0.5592
SCAMP5 Layer 4 2.1348 0.5589
SNAP91 Layer 4 2.3340 0.5587
BASP1 Layer 4 2.3496 0.5578
TUBB2A Layer 6 2.4082 0.5571
APBB1 Layer 4 2.4512 0.5567
CLSTN1 Layer 6 2.1777 0.5560
ENO2 Layer 4 2.5332 0.5553
TPPP Layer 5 2.2168 0.5552
DYNLRB1 Layer 4 2.1719 0.5546
SNX10 Layer 5 2.1152 0.5542
SYN2 Layer 4 2.5508 0.5542
SLC17A7 Layer 4 2.2461 0.5541
ELAVL4 Layer 4 2.2832 0.5532
PPP2R1A Layer 5 2.2930 0.5530
ATP5F1B Layer 5 2.2422 0.5525
ATP2B2 Layer 4 2.4512 0.5523
GNAO1 Layer 4 2.1914 0.5517
ATP6V0A1 Layer 5 2.2676 0.5504
NAP1L2 Layer 4 2.2324 0.5502
GAP43 Layer 6 2.2324 0.5487
YWHAG Layer 6 2.2871 0.5485
ATP5F1A Layer 4 2.1152 0.5483
CFL1 Layer 6 2.0586 0.5470
APP Layer 4 2.1191 0.5469
CELF4 Layer 5 2.3867 0.5467
SNCA Layer 6 2.5957 0.5465

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1836
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1836_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1836/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1836/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1836/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1836/report/PD/BN1836_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1836/report/PD/BN1836_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:13:28
  • Number of Processes: 10
  • Spending Time: 0h 3m